BN1535 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 2.3422e-06 5.4091e-04
Layer 4 1.4996e-05 7.7240e-05
Layer 5 1.5953e-05 3.8261e-04
Layer 6 4.9770e-05 6.3092e-04
Layer 2 3.1023e-04 7.2600e-03
Layer 1 6.3313e-01 5.7298e-01
WM 9.9850e-01 5.5964e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
TAGLN3 Expression Distribution
Gene Specificity Score (GSS)
TAGLN3 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
TAGLN3 Layer 5 2.7852 0.8496
TOLLIP Layer 4 2.9668 0.8412
GPI Layer 4 2.7822 0.8407
STMN2 Layer 5 3.0117 0.8401
NDRG4 Layer 4 2.9863 0.8395
SYP Layer 5 2.9473 0.8393
ATP6V1B2 Layer 4 3.0059 0.8382
APLP2 Layer 5 2.7852 0.8380
ATP1A3 Layer 5 2.7539 0.8360
SNAP91 Layer 5 3.0781 0.8352
SERPINI1 Layer 4 2.9023 0.8351
RAB3A Layer 5 2.8027 0.8344
SULT4A1 Layer 4 3.0088 0.8343
CNTN1 Layer 6 2.7305 0.8338
YPEL3 Layer 4 2.8594 0.8338
ANK2 Layer 4 2.6426 0.8324
GHITM Layer 5 2.7539 0.8324
ATP2B2 Layer 4 2.7598 0.8323
CALY Layer 4 2.9219 0.8323
EEF1A2 Layer 4 2.7539 0.8314
SNCA Layer 6 2.9863 0.8309
PGAM1 Layer 5 2.5957 0.8304
PFN2 Layer 4 3.0859 0.8304
GNG3 Layer 6 2.7129 0.8301
PNMA2 Layer 4 2.7715 0.8300
TERF2IP Layer 4 2.7334 0.8300
STMN3 Layer 4 2.6719 0.8296
CLIP3 Layer 5 2.6543 0.8295
GAP43 Layer 5 2.7715 0.8289
ATP2A2 Layer 5 2.7305 0.8288
CABP1 Layer 5 2.9473 0.8286
SLC25A3 Layer 4 2.6074 0.8285
SV2A Layer 4 3.0059 0.8284
INPP5F Layer 4 3.0254 0.8283
NDUFB1 Layer 5 2.5566 0.8283
PRKAR1B Layer 4 2.9473 0.8278
RAB6B Layer 4 2.7422 0.8278
WBP2 Layer 4 2.5840 0.8274
NPTN Layer 4 2.7793 0.8263
LMO4 Layer 6 2.7910 0.8259
ARF1 Layer 4 2.8281 0.8258
GNB1 Layer 5 2.5781 0.8256
SIRPA Layer 5 2.7363 0.8255
TUBA4A Layer 4 3.0029 0.8254
NAPB Layer 5 2.6895 0.8252
PAFAH1B1 Layer 5 2.5391 0.8247
VAMP2 Layer 5 2.6309 0.8246
BEX2 Layer 5 2.8594 0.8245
SYN1 Layer 4 2.8828 0.8245
SV2B Layer 6 2.8652 0.8243

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1535
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1535_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1535/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1535/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1535/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1535/report/PD/BN1535_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1535/report/PD/BN1535_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:50:13
  • Number of Processes: 10
  • Spending Time: 0h 4m